We used a marker derived from a cDNA clone of Nipponbare. The position of the locus has been identified by examining a recombination value between Nipponbare and Kasalath experimentally. An annotation for the sequence of the marker was estimated using a protein database. 1174 points are discrete positions on the map; each chromosome, 159, 129, 148, 95, 107, 104, 88, 83, 54, 68, 79, 60.

The 186 F2 plant mapping population used was derived from rice cultivars Nipponbare and Kasalath.

The main sources of the markers in this map derives from various cDNA libraries of Nipponbare, and markers are indicated by clone names denoted with C, R, G, Y, L, P, T, W, B, M, V or TEL numbers.

The first letter of the marker name indicates the category of mapped clones as follows:
C, cDNA clones derived from callus library;
R, cDNAs from root library;
G, random genomic clones;
Y, YAC-end clones;
L, NotI-linking clones;
P, randomly amplified polymorphic DNAs;
T, STS markers;
W, wheat clones;
B, barley clones;
M, maize clones;
TEL, telomere-associated sequences;
S, cDNAs from etiolated shoot (S with numbers < 10,000) and green shoot (S with numbers > 10,000);
F, cDNAs from shoot of a near-isogenic line;
and V and other symbols (Ky4, Kyu08, Kyy03, SINE1_r6), clones derived from other rice varieties.

W numbers correspond to the PSR numbers of clones developed by M. D. Gale (John Innes Centre, UK). Markers denoted with a V contain both genomic and cDNA clones including SINE1r6 isolated in other works. Letters A, B, C and D following the clone number indicate that those loci were assigned by mapping with one of the polymorphic DNA fragments of the multiple copy sequences. L and R following the Y number marker indicate left and right end clones, respectively, of YAC clones.

Name etc of protein coded by determination of location of RFLP markers were estimated by a similarity search in both the PIR (Rel.48.0) and SWISS-PROT (Rel.33) protein databases.

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